GREMLIN Database
TRUA - tRNA pseudouridine synthase A
UniProt: P70973 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 247 (242)
Sequences: 5652 (3986)
Seq/√Len: 256.2

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
155_T167_K3.0141.00
108_K244_Y2.9751.00
110_E188_T2.7451.00
147_H218_K2.5711.00
29_E32_K2.3021.00
130_Y205_L2.2961.00
156_S223_A2.2841.00
108_K188_T2.2541.00
151_T170_T2.2371.00
19_V31_E2.1321.00
142_R146_K2.0981.00
15_N23_K2.0981.00
218_K222_E2.0971.00
110_E186_R2.0821.00
212_I216_E2.0741.00
28_D32_K2.0611.00
24_R29_E2.0291.00
13_L87_D1.9531.00
112_R241_W1.9171.00
112_R184_Q1.8931.00
216_E219_S1.8721.00
203_T217_V1.8631.00
112_R186_R1.8611.00
141_M208_G1.8521.00
143_E214_P1.8411.00
185_M201_A1.8341.00
114_F239_Y1.8031.00
77_P93_A1.7981.00
27_Q31_E1.7801.00
146_K149_I1.7771.00
174_L185_M1.7251.00
196_M200_I1.7051.00
240_L243_V1.7051.00
4_K94_E1.7011.00
59_A241_W1.6971.00
64_H102_A1.6931.00
187_I200_I1.6841.00
117_T178_E1.6331.00
89_A121_P1.6171.00
174_L187_I1.6171.00
177_T186_R1.6141.00
147_H214_P1.5961.00
213_S216_E1.5911.00
173_E188_T1.5901.00
5_C63_I1.5821.00
17_Y63_I1.5741.00
36_V83_L1.5611.00
108_K172_Y1.5391.00
134_Y209_I1.5381.00
14_F87_D1.5381.00
171_I187_I1.5331.00
145_A174_L1.5251.00
14_F24_R1.5161.00
35_A43_R1.4871.00
4_K62_V1.4761.00
110_E244_Y1.4711.00
19_V28_D1.4661.00
7_I63_I1.4631.00
206_D211_K1.4501.00
8_S91_K1.4421.00
145_A204_L1.4381.00
114_F182_G1.4241.00
3_L67_T1.4221.00
10_D128_Y1.4201.00
24_R87_D1.4081.00
137_N210_G1.3931.00
12_H127_H1.3751.00
137_N140_D1.3551.00
3_L93_A1.3521.00
203_T230_G1.3241.00
172_Y190_S1.3231.00
148_L200_I1.3171.00
30_L90_V1.3081.00
46_V63_I1.3041.00
139_Q142_R1.3011.00
114_F184_Q1.3001.00
6_T62_V1.2981.00
10_D127_H1.2971.00
29_E88_I1.2951.00
42_D68_P1.2821.00
206_D212_I1.2771.00
169_R191_G1.2761.00
145_A176_W1.2621.00
142_R175_D1.2511.00
142_R176_W1.2461.00
19_V45_P1.2421.00
15_N54_S1.2311.00
17_Y48_S1.2261.00
172_Y188_T1.2251.00
151_T190_S1.2211.00
30_L63_I1.2151.00
6_T92_Q1.2151.00
115_V185_M1.2031.00
107_V246_D1.2011.00
12_H57_H1.1851.00
13_L127_H1.1721.00
195_N199_I1.1681.00
140_D210_G1.1661.00
9_Y61_Q1.1441.00
110_E241_W1.1441.00
188_T244_Y1.1361.00
144_A207_A1.1231.00
143_E146_K1.1181.00
136_L141_M1.1161.00
10_D126_R1.1161.00
225_D228_A1.1151.00
32_K36_V1.1121.00
149_I173_E1.1061.00
49_S61_Q1.1041.00
122_D125_K1.0981.00
130_Y233_A1.0971.00
187_I201_A1.0941.00
116_Y129_A1.0911.00
151_T168_V1.0791.00
6_T60_G1.0711.00
220_M223_A1.0671.00
125_K182_G1.0631.00
223_A228_A1.0631.00
158_C167_K1.0621.00
31_E46_V1.0601.00
138_V178_E1.0581.00
122_D129_A1.0571.00
130_Y234_P1.0571.00
72_P75_R1.0551.00
140_D143_E1.0531.00
147_H215_D1.0461.00
24_R28_D1.0441.00
207_A217_V1.0431.00
213_S217_V1.0431.00
118_E181_D1.0421.00
143_E215_D1.0351.00
60_G242_N1.0261.00
7_I30_L1.0241.00
50_G61_Q1.0231.00
176_W185_M1.0221.00
110_E242_N1.0221.00
96_A99_G1.0171.00
101_H104_F1.0081.00
138_V183_L1.0031.00
140_D214_P1.0011.00
15_N25_T0.9991.00
177_T184_Q0.9971.00
195_N232_T0.9961.00
5_C93_A0.9911.00
8_S123_V0.9881.00
5_C65_F0.9871.00
14_F88_I0.9811.00
144_A214_P0.9771.00
144_A208_G0.9751.00
73_A93_A0.9741.00
156_S224_K0.9741.00
8_S122_D0.9721.00
178_E181_D0.9711.00
132_F209_I0.9701.00
75_R79_A0.9661.00
4_K96_A0.9631.00
117_T183_L0.9571.00
199_I232_T0.9571.00
226_R230_G0.9551.00
153_D167_K0.9491.00
178_E183_L0.9431.00
130_Y236_H0.9411.00
47_V64_H0.9411.00
205_L233_A0.9391.00
128_Y239_Y0.9361.00
14_F26_V0.9351.00
25_T28_D0.9341.00
141_M204_L0.9331.00
159_A195_N0.9331.00
140_D213_S0.9301.00
174_L204_L0.9291.00
115_V205_L0.9161.00
37_L83_L0.9111.00
142_R178_E0.9081.00
174_L200_I0.9041.00
4_K100_F0.9041.00
6_T94_E0.8981.00
49_S243_V0.8941.00
157_F220_M0.8931.00
80_L90_V0.8931.00
187_I197_V0.8921.00
176_W183_L0.8761.00
175_D186_R0.8691.00
26_V88_I0.8641.00
73_A95_I0.8611.00
138_V142_R0.8560.99
75_R78_Y0.8560.99
106_A243_V0.8540.99
212_I220_M0.8530.99
226_R229_A0.8500.99
37_L76_W0.8490.99
186_R241_W0.8480.99
95_I98_D0.8460.99
42_D67_T0.8410.99
64_H101_H0.8400.99
55_G235_G0.8340.99
206_D209_I0.8310.99
116_Y122_D0.8310.99
44_I65_F0.8270.99
129_A182_G0.8210.99
125_K129_A0.8160.99
34_L65_F0.8130.99
202_G230_G0.8130.99
158_C162_T0.8120.99
109_K191_G0.8100.99
148_L217_V0.8040.99
148_L174_L0.8020.99
38_H67_T0.7980.99
173_E186_R0.7980.99
158_C161_K0.7970.99
215_D219_S0.7970.99
132_F205_L0.7950.99
219_S228_A0.7930.99
176_W204_L0.7920.99
161_K194_Y0.7840.99
136_L205_L0.7750.99
214_P217_V0.7740.99
206_D231_R0.7710.99
203_T229_A0.7640.99
155_T158_C0.7600.99
37_L79_A0.7600.99
125_K128_Y0.7600.99
48_S63_I0.7600.99
38_H44_I0.7520.99
15_N22_G0.7510.99
34_L80_L0.7510.99
81_N89_A0.7500.99
7_I17_Y0.7490.99
115_V201_A0.7450.99
59_A239_Y0.7390.98
49_S245_Y0.7300.98
204_L208_G0.7290.98
170_T190_S0.7280.98
153_D224_K0.7270.98
171_I189_G0.7240.98
114_F125_K0.7220.98
159_A194_Y0.7220.98
139_Q143_E0.7180.98
47_V101_H0.7160.98
109_K240_L0.7140.98
38_H76_W0.7120.98
31_E45_P0.7030.98
30_L46_V0.7030.98
33_A83_L0.7030.98
215_D218_K0.6990.98
141_M176_W0.6990.98
67_T76_W0.6990.98
216_E220_M0.6980.98
171_I174_L0.6930.98
159_A232_T0.6920.98
205_L209_I0.6900.98
220_M229_A0.6810.97
199_I226_R0.6770.97
35_A38_H0.6770.97
142_R174_L0.6760.97
49_S106_A0.6730.97
179_T184_Q0.6730.97
14_F29_E0.6690.97
29_E33_A0.6680.97
17_Y46_V0.6650.97
77_P92_Q0.6650.97
156_S225_D0.6640.97
50_G240_L0.6630.97
115_V183_L0.6610.97
113_Y233_A0.6610.97
38_H43_R0.6600.97
148_L171_I0.6530.97
102_A105_S0.6520.97
60_G91_K0.6520.97
219_S223_A0.6510.97
141_M145_A0.6490.97
27_Q46_V0.6480.97
144_A204_L0.6420.96
6_T91_K0.6380.96
74_E78_Y0.6350.96
78_Y82_A0.6330.96
147_H217_V0.6330.96
138_V176_W0.6290.96
220_M230_G0.6260.96
63_I90_V0.6240.96
50_G243_V0.6240.96
34_L38_H0.6200.96
199_I229_A0.6180.96
117_T132_F0.6170.95
124_F128_Y0.6150.95
219_S222_E0.6110.95
206_D230_G0.6100.95
164_V167_K0.6080.95
176_W187_I0.6050.95
201_A233_A0.6030.95
148_L221_L0.6010.95
152_H168_V0.6000.95
117_T181_D0.5990.95
147_H213_S0.5980.95
62_V245_Y0.5960.95
116_Y125_K0.5950.94
158_C164_V0.5930.94
143_E147_H0.5910.94
57_H237_G0.5910.94
42_D69_L0.5900.94
153_D168_V0.5860.94
115_V136_L0.5860.94
207_A216_E0.5860.94
214_P218_K0.5840.94
8_S124_F0.5840.94
217_V221_L0.5820.94
59_A114_F0.5820.94
114_F241_W0.5810.94
156_S228_A0.5800.94
213_S219_S0.5760.94
127_H236_H0.5740.93
156_S229_A0.5720.93
136_L208_G0.5710.93
33_A80_L0.5700.93
73_A77_P0.5700.93
169_R190_S0.5660.93
147_H207_A0.5630.93
109_K189_G0.5630.93
106_A109_K0.5620.93
76_W93_A0.5620.93
140_D207_A0.5620.93
50_G105_S0.5610.93
155_T224_K0.5590.92
107_V244_Y0.5580.92
241_W244_Y0.5550.92
47_V102_A0.5500.92
5_C34_L0.5480.92
69_L76_W0.5480.92
50_G102_A0.5450.92
14_F84_L0.5430.91
23_K28_D0.5430.91
7_I61_Q0.5410.91
35_A44_I0.5400.91
109_K195_N0.5380.91
77_P120_H0.5340.91
189_G199_I0.5320.91
85_P88_I0.5310.90
19_V32_K0.5310.90
156_S220_M0.5280.90
203_T220_M0.5280.90
3_L95_I0.5270.90
101_H245_Y0.5270.90
158_C193_L0.5270.90
70_S95_I0.5270.90
199_I230_G0.5260.90
20_Q25_T0.5240.90
128_Y131_H0.5240.90
229_A232_T0.5230.90
71_I75_R0.5190.89
30_L34_L0.5140.89
36_V39_K0.5130.89
29_E84_L0.5110.89
81_N84_L0.5100.89
189_G192_F0.5100.89
15_N24_R0.5080.88
87_D126_R0.5060.88
35_A42_D0.5050.88
185_M204_L0.5050.88
172_Y189_G0.5040.88
39_K69_L0.5030.88
149_I152_H0.5030.88
13_L24_R0.5020.88
38_H69_L0.5000.88
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
1dj0A 2 0.9919 100 0.015 Contact Map
1vs3A 2 0.9838 100 0.024 Contact Map
4j37A 1 0.9514 100 0.076 Contact Map
2v9kA 1 0.8502 94.7 0.922 Contact Map
2l0cA 1 0.1336 11.6 0.965 Contact Map
1z2zA 1 0.9433 7.7 0.968 Contact Map
4kw3A 1 0.5101 6.5 0.969 Contact Map
4kt0E 1 0.1498 5.3 0.97 Contact Map
3rd4A 3 0.0972 5.1 0.971 Contact Map
1jb0E 1 0.1377 5.1 0.971 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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